[ImageJ-devel] [VIGRA] Avian VM and Bio-Formats

[Ullrich Koethe]

Hi Johannes,

 >> In vigra-imglib2 (branch 'wip'), 'mvn install' compiles and produces a
 >> number of compiler warnings which seem to be uncritical on first glance,
 >> but are confusingly flagged as "[ERROR]" in the maven output.
 >
 > Which ones? (Please just paste such errors when you encounter them, of
 > course I could reproduce, if only I had more time!)
 >

These warnings are related to VIGRA itself, so there is no need for you 
to act on them. I merely complained about the fact that warnings are 
flagged as [ERROR] by maven. In fact, that's not quite precise: The 
actual warning is correctly flagged as [WARNING], but the preceding 
diagnostic lines which merely provide template instantiation context 
(i.e. the call stack leading up to the warning) are flagged as [ERROR]. 
It would be much better to flag them as [CONTEXT] or similar.

[ERROR] In file included from 
/home/ukoethe/src/vigra-imglib2/src/main/cxx/VigraImg3DUnsignedByte.cxx:2:0:
...
[ERROR] 
/home/ukoethe/src/vigra-imglib2/src/main/cxx/VigraImg3DUnsignedByte.cxx:54:45: 
   required from here
[WARNING] 
/home/ukoethe/vigra-git/vigra/include/vigra/multi_array.hxx:3194:55: 
warning: conversion to 'int' from 'vigra::MultiArrayView<2u, unsigned 
char, vigra::StridedArrayTag>::difference_type_1 {aka long int}' may 
alter its value [-Wconversion]

In the meantime, the error message produced by ./avian-run.sh changed. 
But it looks like the same problem as before.

java.lang.ExceptionInInitializerError
   at net.imglib2.vigra.VigraImgFactory3DUnsignedByte.create (line 19)
   at net.imglib2.vigra.VigraImgFactory3DUnsignedByte.create (line 14)
   at io.scif.img.ImgOpener.openImg (line 301)
   at io.scif.img.ImgOpener.openImg (line 217)
   at io.scif.img.ImgOpener.openImg (line 200)
   at Example.main (line 34)
   at Example.main (line 22)
caused by: java.lang.UnsatisfiedLinkError: library not found: 
/home/ukoethe/src/vigra-imglib2/target/nar/vigra-imglib2-1.0.0-SNAPSHOT-amd64-Linux-gpp-jni/lib/amd64-Linux-gpp/jni/libvigra-imglib2-1.0.0-SNAPSHOT.so
   at java.lang.Runtime.load
   at java.lang.Runtime.load (line 32)
   at java.lang.System.load (line 117)
   at net.imglib2.vigra.NarHelper.loadLibrary (line 75)
   at net.imglib2.vigra.VigraImg3DUnsignedByte.<clinit> (line 23)
   at net.imglib2.vigra.VigraImgFactory3DUnsignedByte.create (line 19)
   at net.imglib2.vigra.VigraImgFactory3DUnsignedByte.create (line 14)
   at io.scif.img.ImgOpener.openImg (line 301)
   at io.scif.img.ImgOpener.openImg (line 217)
   at io.scif.img.ImgOpener.openImg (line 200)
   at Example.main (line 34)
   at Example.main (line 22)

The library it complains about exists:

 >> ls -l 
/home/ukoethe/src/vigra-imglib2/target/nar/vigra-imglib2-1.0.0-SNAPSHOT-amd64-Linux-gpp-jni/lib/amd64-Linux-gpp/jni/libvigra-imglib2-1.0.0-SNAPSHOT.so

-rwxr-xr-x 1 ukoethe ukoethe 122627 Dec  9 14:51 
/home/ukoethe/src/vigra-imglib2/target/nar/vigra-imglib2-1.0.0-SNAPSHOT-amd64-Linux-gpp-jni/lib/amd64-Linux-gpp/jni/libvigra-imglib2-1.0.0-SNAPSHOT.so

Best regards
Ulli